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I think it was shown around that time, when the two of them were walking around sewers or something.

Nope, that was Nibi. I'm pretty sure that in manga only beginning of the fight with Sanbi is shown, so there's a huge chance that they do same thing in anime, or simply omit that - after all, nothing big was shown there.

well if you watched the anime its pretty much the exact same, which is rare for adaptations, the only difference in anime vs manga, is that there is no fillers, I'm pretty sure they didn't change any of the story, though in the manga there is Kakashi Gaiden which seems to have been skipped over by the anime but I'm not sure, please somebody confirm this for me.

That would have worked, but it still would have been out of place, the reason why they didn't do after filler was because viewership dropped dramatically after non canon episodes were broadcast, and with shippuden it would be awkard because timeskip, represented change where as kakashi gaiden is firmly in the past, plus the first episode with naruto standing on top of the village was a great way to have the series be reborn, to escape the mess that were the fillers. I'm still hoping that they will eventually do kakashi gaiden, either in movie or ova form, or hell even in the show as a way to space out manga from anime. Kakashi gaiden was one of the better parts of the anime, because one, we get to see a scrub uchiha, yondaime, and of course chibi kakashi.